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- PDB-2cmf: Torpedo californica acetylcholinesterase complexed with alkylene-... -

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Basic information

Entry
Database: PDB / ID: 2cmf
TitleTorpedo californica acetylcholinesterase complexed with alkylene- linked bis-tacrine dimer (5 carbon linker)
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE ESTERASE / SERINE HYDROLASE / ALZHEIMER'S DISEASE / NERVE / MUSCLE / SYNAPSE / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CHOLINESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Acetylcholinesterase, fish/snake / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F11 / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsRydberg, E.H. / Brumshtein, B. / Greenblatt, H.M. / Wong, D.M. / Pang, Y.P. / Silman, I. / Sussman, J.L.
CitationJournal: J. Med. Chem. / Year: 2006
Title: Complexes of alkylene-linked tacrine dimers with Torpedo californica acetylcholinesterase: Binding of Bis5-tacrine produces a dramatic rearrangement in the active-site gorge.
Authors: Rydberg, E.H. / Brumshtein, B. / Greenblatt, H.M. / Wong, D.M. / Shaya, D. / Williams, L.D. / Carlier, P.R. / Pang, Y.P. / Silman, I. / Sussman, J.L.
History
DepositionMay 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Feb 13, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2324
Polymers61,3251
Non-polymers9073
Water2,882160
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4648
Polymers122,6502
Non-polymers1,8146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4830 Å2
ΔGint-9 kcal/mol
Surface area37730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.153, 113.153, 136.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-F11 / N,N'-DI-1,2,3,4-TETRAHYDROACRIDIN-9-YLPENTANE-1,5-DIAMINE


Mass: 464.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H36N4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESPONSIBLE FOR THE PROMPT HYDROLYSIS OF CHOLINE PRESENT IN THE SYNAPSE.IT ALSO TAKES PART IN ...RESPONSIBLE FOR THE PROMPT HYDROLYSIS OF CHOLINE PRESENT IN THE SYNAPSE.IT ALSO TAKES PART IN INTERCELLULAR INTERACTIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 277 K / pH: 5.8
Details: 28-33% V/V PEG 200, 0.5MM MES PH5.8, 4DEG C, SEEDING, pH 5.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 34257 / % possible obs: 96.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.5→29.47 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1867965.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: THE BIOLOGICALLY ACTIVE FORM OF THIS MOLECULE IS A DIMER, FORMED BY ROTATING THE ASYMMETRIC UNIT ABO THE CRYSTALLOGRAPHIC TWO-FOLD AXIS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1710 5 %RANDOM
Rwork0.214 ---
obs0.214 34351 96.7 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 55.8345 Å2 / ksol: 0.330316 e/Å3
Displacement parametersBiso mean: 67.22 Å2
Baniso -1Baniso -2Baniso -3
1-21.02 Å29.82 Å20 Å2
2--22.32 Å20 Å2
3----43.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 63 160 4395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it8.372
X-RAY DIFFRACTIONc_scangle_it9.272.5
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rfree0.2 45 4.5 %
Rwork0.18 945 -

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